What's a ".cmd" file? (Okay, it has variables, so it's probably like some sort of executable script. If so, what language does it use?) Are the variables that it contains like shell environment variables (similar to "PATH")? Do you have the ability/desire to edit the .cmd file if necessary so that it plays nicely with a perl script? (Whatever the .cmd file does, have you considered replacing it completely with a perl script?)

Have you tried any sort of perl script on your own yet? If so, why not post it as an update or reply to your node, with some clear information about what its inputs are, and what you intend it to do (and what it actually does, if it doesn't do what you want).

Sorry, I have no answers, just questions. Your post was a bit vague.